qhgenomics Goto Github PK

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

confindr

Intra-species bacterial contamination detection

fastqc

A quality control analysis tool for high throughput sequencing data

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

hap-eval

A VCF comparison engine for structual variant benchmarking

hello

Classic hello world script in Nextflow language

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

kraken2

The second version of the Kraken taxonomic sequence classification system

mlst

:id: Scan contig files against PubMLST typing schemes

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

pneumocat

Pneumococcal Capsular Typing tool for NGS data

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

resfinder

roary

Rapid large-scale prokaryote pan genome analysis

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

sars-cov-2_sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

sentieon-cwl

CWL pipelines for the Sentieon tools

sentieon-dnascope-ml

Sentieon DNAscope + Machine Learning Model

sentieon-dnaseq

Sentieon DNAseq

sentieon-docker

Example Dockerfiles for use with the Sentieon software

sentieon-google-genomics

Run Sentieon pipelines on Google Cloud Platform

sentieon-matching-performance

Accuracy and runtime benchmarks for the Sentieon GATK-matching tools

sentieon-scripts

Helper scripts for biological data processing from Sentieon

sentieon-wdl

WDL pipelines for the Sentieon tools

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

spades

SPAdes Genome Assembler

sra-tools

SRA Tools